I want to perform global sequence alignment on 3 DNA sequences. Now while making the scoring matrix for the dynamic programming, there are 7 possible cases. In case of 2 DNA sequences, the options are either a match or a insert or delete. But in 3 sequence alignment, there are all three match, two match and a gap and two gaps.
Is the following observation of mine is right?
1. For exact match in three sequence I just add the matching score in the scoring matrix
2. For two match and a gap I added (matched scored + gap) (i.e. matched score = 2, gap = -2)
3. For two gaps I added (gap * 2) in the scoring matrix.
Is these observation correct?